Thanks to technological advances in high-density genome scans, genetic association studies routinely have data for hundreds of thousand or millions of genetic markers across the entire genome. Despite these advancements, the mapping of many complex traits has proven to be difficult, illustrating the need for new and more powerful methods for the identification of loci that influence complex traits. Statistical methods for the analysis of genetic data have primarily been developed for markers on the autosomal chromosomes and significantly less attention has been given to the analysis of the X-chromosome, despite the potential for identifying X-linked genes that influence complex traits. This project is concerned with development and application of statistical methodology for the analysis of X-chromosome data. We will develop statistical methodology for association testing of X-linked variants in samples with related individuals as well as methodology for relatedness inference on the X. We will also develop statistical methodology for estimating and adjusting for population structure on the X-chromosome in samples from populations with admixed ancestry, such as African Americans and Hispanics.